Eye and skin infections caused by "Acanthamoeba spp." are generally treatable. Topical use of 0.1% propamidine isethionate (Brolene) plus neomycin-polymyxin B-gramicidin ophthalmic solution has been a successful approach; keratoplasty is often necessary in severe infections. Although most cases of brain (CNS) infection with "Acanthamoeba" have resulted in death, patients have recovered from the infection with proper treatment.

In one case, cloxacillin, ceftriaxone, and amphotericin B were tried.

Two patients survived after being successfully treated with a therapy consisting of flucytosine, pentamidine, fluconazole, sulfadiazine and azithromycin. Thioridazine was also given. Successful treatment in these cases was credited to "awareness of "Balamuthia" as the causative agent of encephalitis and early initiation of antimicrobial therapy."

Even with treatment, the condition is often fatal, and there are very few recorded survivors, almost all of whom suffered permanent neurocognitive deficits. Antifungal drugs including ketoconazole, miconazole, 5-flucytosine and pentamidine have been shown to be effective against GAE-causing organisms in laboratory tests.

Free-living amoebae (or "FLA") in the Amoebozoa group are important causes of disease in humans and animals.

"Naegleria fowleri" is sometimes included in the group "free-living amoebae", and it causes a condition traditionally called primary amoebic meningoencephalitis. However, Naegleria is now considered part of the Excavata, not the Amoebozoa, and is considered to be much more closely related to "Leishmania" and "Trypanosoma".

Yersiniosis is usually self-limiting and does not require treatment. For severe infections (sepsis, focal infection) especially if associated with immunosuppression, the recommended regimen includes doxycycline in combination with an aminoglycoside. Other antibiotics active against "Y. enterocolitica" include trimethoprim-sulfamethoxasole, fluoroquinolones, ceftriaxone, and chloramphenicol. "Y. enterocolitica" is usually resistant to penicillin G, ampicillin, and cephalotin due to beta-lactamase production.

"Toxoplasma" infection can be prevented in large part by:

- cooking meat to a safe temperature (i.e., one sufficient to kill "Toxoplasma")

- peeling or thoroughly washing fruits and vegetables before eating

- cleaning cooking surfaces and utensils after they have contacted raw meat, poultry, seafood, or unwashed fruits or vegetables

- pregnant women avoiding changing cat litter or, if no one else is available to change the cat litter, using gloves, then washing hands thoroughly

- not feeding raw or undercooked meat to cats to prevent acquisition of "Toxoplasma"

Prolonged and intense rainfall periods are significantly associated with the reactivation of toxoplasmic retinochoroiditis. Changes promoted by this climatic condition concern both the parasite survival in the soil as well as a putative effect on the host immune response due to other comorbidities.

The treatment of TB meningitis is isoniazid, rifampicin, pyrazinamide and ethambutol for two months, followed by isoniazid and rifampicin alone for a further ten months. Steroids help reduce the risk of death in those without HIV. Steroids can be used in the first six weeks of treatment, A few people may require immunomodulatory agents such as thalidomide. Hydrocephalus occurs as a complication in about a third of people with TB meningitis. The addition of aspirin may reduce or delay mortality, possibly by reducing complications such as infarcts.

The treatment includes lowering the increased intracranial pressure and starting intravenous antibiotics (and meanwhile identifying the causative organism mainly by blood culture studies).

Hyperbaric oxygen therapy (HBO2 or HBOT) is indicated as a primary and adjunct treatment which provides four primary functions.

Firstly, HBOT reduces intracranial pressure. Secondly, high partial pressures of oxygen act as a bactericide and thus inhibits the anaerobic and functionally anaerobic flora common in brain abscess. Third, HBOT optimizes the immune function thus enhancing the host defense mechanisms and fourth, HBOT has been found to be of benefit when brain abscess is concomitant with cranial osteomyleitis.

Secondary functions of HBOT include increased stem cell production and up-regulation of VEGF which aid in the healing and recovery process.

Surgical drainage of the abscess remains part of the standard management of bacterial brain abscesses. The location and treatment of the primary lesion also crucial, as is the removal of any foreign material (bone, dirt, bullets, and so forth).

There are few exceptions to this rule: "Haemophilus influenzae" meningitis is often associated with subdural effusions that are mistaken for subdural empyemas. These effusions resolve with antibiotics and require no surgical treatment. Tuberculosis can produce brain abscesses that look identical to conventional bacterial abscesses on CT imaging. Surgical drainage or aspiration is often necessary to identify "Mycobacterium tuberculosis", but once the diagnosis is made no further surgical intervention is necessary.

CT guided stereotactic aspiration is also indicated in the treatment of brain abscess.

The disease is associated with high rates of mortality and severe morbidity.

Alternariosis is an infection by alternaria, presenting cutaneously as focal, ulcerated papules and plaques.

Treatment with itraconazole has been reported.

Fungi and parasites may also cause the disease. Fungi and parasites are especially associated with immunocompromised patients. Other causes include: "Nocardia asteroides", "Mycobacterium", Fungi (e.g. "Aspergillus", "Candida", "Cryptococcus", "Mucorales", "Coccidioides", "Histoplasma capsulatum", "Blastomyces dermatitidis", "Bipolaris", "Exophiala dermatitidis", "Curvularia pallescens", "Ochroconis gallopava", "Ramichloridium mackenziei", "Pseudallescheria boydii"), Protozoa (e.g. "Toxoplasma gondii", "Entamoeba histolytica", "Trypanosoma cruzi", "Schistosoma", "Paragonimus"), and Helminths (e.g. "Taenia solium"). Organisms that are most frequently associated with brain abscess in patients with AIDS are poliovirus, "Toxoplasma gondii", and "Cryptococcus neoformans", though in infection with the latter organism, symptoms of meningitis generally predominate.

These organisms are associated with certain predisposing conditions:

- Sinus and dental infections—Aerobic and anaerobic streptococci, anaerobic gram-negative bacilli (e.g. "Prevotella", "Porphyromonas", "Bacteroides"), "Fusobacterium", "S. aureus", and Enterobacteriaceae

- Penetrating trauma—"S. aureus", aerobic streptococci, Enterobacteriaceae, and "Clostridium" spp.

- Pulmonary infections—Aerobic and anaerobic streptococci, anaerobic gram-negative bacilli (e.g. "Prevotella", "Porphyromonas", "Bacteroides"), "Fusobacterium", "Actinomyces", and "Nocardia"

- Congenital heart disease—Aerobic and microaerophilic streptococci, and "S. aureus"

- HIV infection—"T. gondii", "Mycobacterium", "Nocardia", "Cryptococcus", and "Listeria monocytogenes"

- Transplantation—"Aspergillus", "Candida", "Cryptococcus", "Mucorales", "Nocardia", and "T. gondii"

- Neutropenia—Aerobic gram-negative bacilli, "Aspergillus", "Candida", and "Mucorales"

Epithelial keratitis is treated with topical antivirals, which are very effective with low incidence of resistance. Treatment of the disease with topical antivirals generally should be continued for 10–14 days. Aciclovir ophthalmic ointment and Trifluridine eye drops have similar effectiveness but are more effective than Idoxuridine and Vidarabine eye drops. Oral acyclovir is as effective as topical antivirals for treating epithelial keratitis, and it has the advantage of no eye surface toxicity. For this reason, oral therapy is preferred by some ophthalmologists.

Ganciclovir and brivudine treatments were found to be equally as effective as acyclovir in a systematic review.

Valacyclovir, a pro-drug of acyclovir likely to be just as effective for ocular disease, can cause thrombotic thrombocytopenic purpura/Hemolytic-uremic syndrome in severely immunocompromised patients such as those with AIDS; thus, it must be used with caution if the immune status is unknown.

Topical corticosteroids are contraindicated in the presence of active herpetic epithelial keratitis; patients with this disease who are using systemic corticosteroids for other indications should be treated aggressively with systemic antiviral therapy.

The effect of interferon with an antiviral agent or an antiviral agent with debridement needs further assessment.

Causative organisms include protozoans, viral and bacterial pathogens.

Specific types include:

"Y. enterocolitica" infections are sometimes followed by chronic inflammatory diseases such as arthritis, erythema nodosum, and reactive arthritis. This is most likely because of some immune-mediated mechanism.

"Y. enterocolitica" seems to be associated with autoimmune Graves-Basedow thyroiditis.

Whilst indirect evidence exists, direct causative evidence is limited,

and "Y. enterocolitica" is probably not a major cause of this disease, but may contribute to the development of thyroid autoimmunity arising for other reasons in genetically susceptible individuals.

"Y. enterocolitica" infection has also been suggested to not be the cause of autoimmune thyroid disease, but rather is only an associated condition, with both having a shared inherited susceptibility.

More recently, the role for "Y. enterocolitica" has been disputed.

Small extramacular lesions (lesions not threatening vision) may be observed without treatment. Sight-threatening lesions are treated for 4–6 weeks with triple therapy consisting of pyrimethamine, sulfadiazine, and folinic acid. During treatment with pyrimethamine, leukocyte and platelet counts should be monitored weekly. Folinic acid protects against the decrease in platelets and white blood cells induced by pyrimethamine.

Prednisone may be used for 3–6 weeks to reduce macular or optic nerve inflammation and can be started on day 3 of antibiotic therapy. Corticosteroids should not be used without concurrent antibiotic treatment or in immunocompromised patients due to the risk of exacerbation of the disease. Currently, there is no published evidence from randomized controlled trials demonstrating that corticosteroids would be an effective adjunct for treating ocular toxoplasmosis.

Trimethoprim-Sulfamethoxazole has been shown to be equivalent to triple therapy in the treatment of ocular toxoplasmosis and may be better tolerated. Clindamycin and azithromycin can also be considered as alternative therapies. Spiramycin may be used safely without undue risk of teratogenicity and may reduce the rate of transmission to the fetus.

AIDS patients require chronic maintenance treatment.

Yersinia pseudotuberculosis is a Gram-negative bacterium that causes Far East scarlet-like fever in humans, who occasionally get infected zoonotically, most often through the food-borne route. Animals are also infected by "Y. pseudotuberculosis". The bacterium is urease positive.

Herpetic stromal keratitis is treated initially with prednisolone drops every 2 hours

accompanied by a prophylactic antiviral drug: either topical antiviral or an oral agent such as acyclovir or valacyclovir. The prednisolone drops are tapered every 1–2 weeks depending on the degree of clinical improvement. Topical antiviral medications are not absorbed by the cornea through an intact epithelium, but orally administered acyclovir penetrates an intact cornea and anterior chamber. In this context, oral acyclovir might benefit the deep corneal inflammation of disciform keratitis.

Tuberculous meningitis is also known as TB meningitis or tubercular meningitis. Tuberculous meningitis is "Mycobacterium tuberculosis" infection of the meninges—the system of membranes which envelop the central nervous system.

In animals, "Y. pseudotuberculosis" can cause tuberculosis-like symptoms, including localized tissue necrosis and granulomas in the spleen, liver, and lymph nodes.

In humans, symptoms of Far East scarlet-like fever are similar to those of infection with "Yersinia enterocolitica" (fever and right-sided abdominal pain), except that the diarrheal component is often absent, which sometimes makes the resulting condition difficult to diagnose. "Y. pseudotuberculosis" infections can mimic appendicitis, especially in children and younger adults, and, in rare cases, the disease may cause skin complaints (erythema nodosum), joint stiffness and pain (reactive arthritis), or spread of bacteria to the blood (bacteremia).

Far East scarlet-like fever usually becomes apparent five to 10 days after exposure and typically lasts one to three weeks without treatment. In complex cases or those involving immunocompromised patients, antibiotics may be necessary for resolution; ampicillin, aminoglycosides, tetracycline, chloramphenicol, or a cephalosporin may all be effective.

The recently described syndrome "Izumi-fever" has been linked to infection with "Y. pseudotuberculosis".

The symptoms of fever and abdominal pain mimicking appendicitis (actually from mesenteric lymphadenitis) associated with "Y. pseudotuberculosis" infection are not typical of the diarrhea and vomiting from classical food poisoning incidents. Although "Y. pseudotuberculosis" is usually only able to colonize hosts by peripheral routes and cause serious disease in immunocompromised individuals, if this bacterium gains access to the blood stream, it has an LD comparable to "Y. pestis" at only 10 CFU.

Treatment is generally supportive. Rest, hydration, antipyretics, and pain or anti-inflammatory medications may be given as needed.

Herpes simplex virus, varicella zoster virus and cytomegalovirus have a specific antiviral therapy. For herpes the treatment of choice is aciclovir.

Surgical management is indicated where there is extremely increased intracranial pressure, infection of an adjacent bony structure (e.g. mastoiditis), skull fracture, or abscess formation.

The majority of people that have viral meningitis get better within 7-10 days.

Currently, no therapeutic drugs are prescribed for the disease. Therefore, prevention is the sole mode of treatment. This disease can only be prevented by quarantining sick birds and preventing migration of birds around the house, causing them to spread the disease. Deworming of birds with anthelmintics can reduce exposure to the cecal nematodes that carry the protozoan. Good management of the farm, including immediate quarantine of infected birds and sanitation, is the main useful strategy for controlling the spread of the parasitic contamination. The only drug used for the control (prophylaxis) in the United States is nitarsone at 0.01875% of feed until 5 days before marketing. Natustat and nitarsone were shown to be effective therapeutic drugs. Nifurtimox, a compound with known antiprotozoal activity, was demonstrated to be significantly effective at 300–400 ppm, and well tolerated by turkeys.

It has been proposed that viral meningitis might lead to inflammatory injury of the vertebral artery wall.

The Meningitis Research Foundation is conducting a study to see if new genomic techniques can the speed, accuracy and cost of diagnosing meningitis in children in the UK. The research team will develop a new method to be used for the diagnosis of meningitis, analysing the genetic material of microorganisms found in CSF (cerebrospinal fluid). The new method will first be developed using CSF samples where the microorganism is known, but then will be applied to CSF samples where the microorganism is unknown (estimated at around 40%) to try and identify a cause.

Healing is prolonged, and usually takes 6–10 weeks. The ulcer heals by secondary intention.

During the 1980s, dentist Hal Huggins, sparking severe controversy, spawned biological dentistry, which claims that conventional tooth extraction routinely leaves within the tooth socket the periodontal ligament that often becomes gangrenous, then, forming a jawbone "cavitation" seeping infectious and toxic material. Sometimes forming elsewhere in bones after injury or ischemia, jawbone cavitations are recognized as foci also in osteopathy and in alternative medicine, but conventional dentists generally conclude them to be nonexistent. Although the International Academy of Oral Medicine & Toxicology claims that the scientific evidence establishing the existence of jawbone cavitations is overwhelming, and even published in textbooks, the diagnosis and related treatment remain controversial, and allegations of quackery persist.

Huggins and many biological dentists also espouse Weston Price's findings on endodontically treated teeth routinely being foci of infection, although these dentists have been accused of quackery. Conventional belief is that microorganisms within inaccessible regions of a tooth's roots are rendered harmless once entrapped by the filling material, although little evidence supports this. A H Rogers in 1976 and E H Ehrmann in 1977 had dismissed any relation between endodontics and focal infection. At dentist George Meinig's 1994 book, "Root Canal Cover-Up Exposed", discussing researches of Rosenow and of Price, some dentistry scholars reasserted that the claims were evaluated and disproved by the 1940s. Yet Meinig was but one of at least three authors who in the early 1990s independently renewed the concern.

Boyd Haley and Curt Pendergrass found especially high levels of bacterial toxins in root-filled teeth. Although such possibility appears especially likely amid compromised immunity—as in individuals cirrhotic, asplenic, elderly, rheumatoid arthritic, or using steroid drugs—there remained a lack of carefully controlled studies definitely establishing adverse systemic effects. Conversely, some if few studies have investigated effects of systemic disease on root-canal therapy's outcomes, which tend to worsen with poor glycemic control, perhaps via impaired immune response, a factor largely ignored until recently, but now recognized as important. Still, even by 2010, "the potential association between systemic health and root canal therapy has been strongly disputed by dental governing bodies and there remains little evidence to substantiate the claims".

The traditional root-filling material is gutta-percha, whereas a new material, Biocalex, drew initial optimism even in alternative dentistry, but Biocalex-filled teeth were later reported by Boyd Haley to likewise seep toxic byproducts of anaerobic bacterial metabolism. Seeking to sterilize the tooth interior, some dentists, both alternative and conventional, have applied laser technology. Although endodontic therapy can fail and eventually often does, dentistry scholars maintain that it "can" be performed without creating focal infections. And even by 2010, molecular methods had rendered no consensus reports of bacteremia traced to asymptomatic endodontic infection. In any event, the predominant view is that shunning endodonthic therapy or routinely extracting endodontically treated teeth to treat or prevent systemic diseases remains unscientific and misguided.

There is as yet inadeqaute data from randomised controlled trials.

Treatment with HAART and ACE inhibitors/Angiotensin receptor blockers has been shown to be beneficial and should be given to all patients unless otherwise contra-indicated. General renoprotective measures and the treatment of the complications of nephrotic syndrome and kidney failure are adjunctive.

Corticosteroid treatment can be useful in patients who do not respond to the above treatment. There is some evidence that ciclosporin might be helpful in selective cases, however further trials are required on both steroids and ciclosporin before these drugs can become standardised treatment if at all.